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Sample GSM557691 Query DataSets for GSM557691
Status Public on Jan 05, 2011
Title Drosophila_larvae_wt_H3K9me2_ChIP-Seq
Sample type SRA
Source name 3rd instart Drosophila larvae
Organism Drosophila melanogaster
Characteristics h3k9me2 antibody: 07-441 Upstate antibody
genotype: wild type
Treatment protocol In vivo experiment of wildtype vs mutant (fly EHMT)
Growth protocol Larvae were cultured on standard medium (cornmeal/sugar/agar) at 25 degrees, 45-60% humidity and 12 hour light/dark cycle
Extracted molecule genomic DNA
Extraction protocol Third instar larvae were homogenized in PBS followed by crosslinking with 1% formaldehyde. Crosslinked chromatin was fragmented by sonicating four times for eight minutes (high power, 30 seconds on/off) with a Bioruptor (Diagenode). Chromatin immunoprecipitation was performed with anti-H3K9me2 antibodies and Prot A/G beads (Santa Cruz) were used to capture antibody bound chromatin.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
Description Chromatin IP against H3K9me2
Data processing Reads (36 bp) were aligned to the fly (Drosophila Melanogaster) reference genome. Sequences were aligned to the human BDGP R5/dm3 reference genome using the Illumina Analysis Pipeline allowing one mismatch. Unless specified otherwise, only the tags uniquely aligning to the genome were considered for further analysis. The 36 bp sequence reads were directionally extended to 300 bp, corresponding to the length of the original fragments used for sequencing. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All ChIP-Seq sequence analyses were conducted based on the Apr. 2006 Drosophila melanogaster draft assembly (BDGP Release 5) with Release 5.12 annotations (Oct. 2008) accessed from the UCSC (assembly April 2006) Genome Browser.
Submission date Jun 18, 2010
Last update date May 15, 2019
Contact name Hendrik Marks
Organization name Radboud University Nijmegen, RIMLS
Department Molecular Biology
Street address Geert Grooteplein 26/28
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
Platform ID GPL9061
Series (1)
GSE22447 ChIP-Seq sequencing of H3K9me2 in third instar Drosophila larvae
SRA SRX022334
BioSample SAMN00015358

Supplementary file Size Download File type/resource
GSM557691_Drosophila_larvae_wt_H3K9me2.bed.gz 38.7 Mb (ftp)(http) BED
GSM557691_Drosophila_larvae_wt_H3K9me2.wig.gz 5.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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